Table 1. Characteristics of systems biology approaches to translational readthrough.

Method	Approach	Potential false positives	Shortcomings and potential false negatives
Phylogenetic approaches	In silico identification of extensions with high coding potential (evaluation based on codon substitutions) and high sequence conservation from pre-aligned genomes	Conserved 3′ elements; method not specific for readthrough; genes not expressed; method requires experimental validation of candidates	Recent evolutionary acquisitions and very short extensions are not detected; lack of information on tissue specificity
Ribosome profiling	Analysis of extensions with ribosomal footprint and reading-frame periodicity from translating ribosomes	Extensions with ribosomal footprint but without reading-frame periodicity	Identification might be difficult in extensions shorter than footprint; genes not expressed in tissue sample
In silico regression model	In silico SCC regression model based on experimental dual reporter analyses	Annotation of premature stop codons as natural stop codons in database; no information on expression levels; experimental validation required	Method does not detect TR depending on more distant cis-elements

The three approaches to the identification of TR discussed in this review have their specific characteristics. Potential false positives/negatives are listed for each systems biology approach.